Vibrational spectroscopy and conformation of peptides, polypeptides, and proteins

Raman spectroscopy study on terephthalamide crystal at high pressures

In this study, we have investigated the structural stability of terephthalamide (TPA) crystal at pressure from ambient to 15 GPa in the diamond anvil cell at room temperature by Raman spectroscopy. Assignment for the Raman vibration modes of TPA crystal at ambient conditions has been performed based on the density functional theory (DFT) calculations. Pressure-induced structural transition was monitored using in-situ Raman spectroscopy. Remarkable changes (including the appearance of new Raman peaks, disappearance of original Raman bands, discontinuous changes in the pressure dependence of some Raman wavenumbers at different pressures) in Raman spectra were observed at approximately 1.3 and 5.2 GPa, provided clear evidences for two pressure-induced phase transitions: phase I to phase II at ∼1.3 GPa, phase II to phase III at ∼5.2 GPa.

Solid-state vibrational circular dichroism for pharmaceutical applications: Polymorphs and cocrystal of sofosbuvir

X-ray diffraction is a commonly used technique in the pharmaceutical industry for the determination of the atomic and molecular structure of crystals. However, it is costly, sometimes time-consuming, and it requires a considerable degree of expertise. Vibrational circular dichroism (VCD) spectroscopy resolves these limitations, while also exhibiting substantial sensitivity to subtle modifications in the conformation and molecular packaging in the solid state. This study showcases VCD's ability to differentiate between various crystal structures of the same molecule (polymorphs, cocrystals). We examined the most effective approach for producing high-quality spectra and unveiled the intricate link between structure and spectrum via quantum-chemical computations. We rigorously assessed, using alanine as a model compound, multiple experimental conditions on the resulting VCD spectra, with the aim of proposing an optimal and efficient procedure. The proposed approach, which yields reliable, reproducible, and artifact-free results with maximal signal-to-noise ratio, was then validated using a set comprising of three amino acids (serine, alanine, tyrosine), one hydroxy acid (tartaric acid), and a monosaccharide (ribose) to mimic active pharmaceutical components. Finally, the optimized approach was applied to distinguish three polymorphs of the antiviral drug sofosbuvir and its cocrystal with piperazine. Our results indicate that solid-state VCD is a prompt, cost-effective, and easy-to-use technique to identify crystal structures, demonstrating potential for application in pharmaceuticals. We also adapted the cluster and transfer approach to calculate the spectral properties of molecules in a periodic crystal environment. Our findings demonstrate that this approach reliably produces solid-state VCD spectra of model compounds. Although for large molecules with many atoms per unit cell, such as sofosbuvir, this approach has to be simplified and provides only a qualitative match, spectral calculations, and energy analysis helped us to decipher the observed differences in the experimental spectra of sofosbuvir.

Label-Free Monitoring of Coculture System Dynamics: Probing Probiotic and Cancer Cell Interactions via Infrared Spectroscopic Imaging

Evaluating the dynamic interaction of microorganisms and mammalian cells is challenging due to the lack of suitable platforms for examining interspecies interactions in biologically relevant coculture conditions. In this work, we demonstrate the interaction between probiotic bacteria (Lactococcus lactis and Escherichia coli) and A498 human cancer cells in vitro, utilizing a hydrogel-based platform in a label-free manner by infrared spectroscopy. The L. lactis strain recapitulated in the compartment system secretes polypeptide molecules such as nisin, which has been reported to trigger cell apoptosis. We propose a mid-infrared (IR) spectroscopic imaging approach to monitor the variation of biological components utilizing kidney cells (A498) as a model system cocultured with bacteria. We characterized the biochemical composition (i.e., nucleic acids, protein secondary structures, and lipid conformations) label-free using an unbiased measurement. Several IR spectral features, including unsaturated fatty acids, β-turns in protein, and nucleic acids, were utilized to predict cellular response. These features were then applied to establish a quantitative relationship through a multivariate regression model to predict cellular dynamics in the coculture system to assess the effect of nisin on A498 kidney cancer cells cocultured with bacteria. Overall, our study sheds light on the potential of using IR spectroscopic imaging as a label-free tool to monitor complex microbe-host cell interactions in biological systems. This integration will enable mechanistic studies of interspecies interactions with insights into their underlying physiological processes.

Relationship between amide ratio assessed by Fourier-transform infrared spectroscopy: A biomarker candidate for polycythemia vera disease

The study utilized Fourier transform infrared (FTIR) spectroscopy coupled with chemometrics to investigate protein composition and structural changes in the blood serum of patients with polycythemia vera (PV). Principal component analysis (PCA) revealed distinct biochemical properties, highlighting elevated absorbance of phospholipids, amides, and lipids in PV patients compared to healthy controls. Ratios of amide I/amide II and amide I/amide III indicated alterations in protein structures. Support vector machine analysis and receiver operating characteristic curves identified amide I as a crucial predictor of PV, achieving 100% accuracy, sensitivity, and specificity, while amide III showed a lower predictive value (70%). PCA analysis demonstrated effective differentiation between PV patients and controls, with key wavenumbers including amide II, amide I, and CH lipid vibrations. These findings underscore the potential of FTIR spectroscopy for diagnosing and monitoring PV.

Raman Spectroscopy Reveals Photobiomodulation-Induced α-Helix to β-Sheet Transition in Tubulins: Potential Implications for Alzheimer's and Other Neurodegenerative Diseases

In small clinical studies, the application of transcranial photobiomodulation (PBM), which typically delivers low-intensity near-infrared (NIR) to treat the brain, has led to some remarkable results in the treatment of dementia and several neurodegenerative diseases. However, despite the extensive literature detailing the mechanisms of action underlying PBM outcomes, the specific mechanisms affecting neurodegenerative diseases are not entirely clear. While large clinical trials are warranted to validate these findings, evidence of the mechanisms can explain and thus provide credible support for PBM as a potential treatment for these diseases. Tubulin and its polymerized state of microtubules have been known to play important roles in the pathology of Alzheimer's and other neurodegenerative diseases. Thus, we investigated the effects of PBM on these cellular structures in the quest for insights into the underlying therapeutic mechanisms. In this study, we employed a Raman spectroscopic analysis of the amide I band of polymerized samples of tubulin exposed to pulsed low-intensity NIR radiation (810 nm, 10 Hz, 22.5 J/cm2 dose). Peaks in the Raman fingerprint region (300-1900 cm-1)-in particular, in the amide I band (1600-1700 cm-1)-were used to quantify the percentage of protein secondary structures. Under this band, hidden signals of C=O stretching, belonging to different structures, are superimposed, producing a complex signal as a result. An accurate decomposition of the amide I band is therefore required for the reliable analysis of the conformation of proteins, which we achieved through a straightforward method employing a Voigt profile. This approach was validated through secondary structure analyses of unexposed control samples, for which comparisons with other values available in the literature could be conducted. Subsequently, using this validated method, we present novel findings of statistically significant alterations in the secondary structures of polymerized NIR-exposed tubulin, characterized by a notable decrease in α-helix content and a concurrent increase in β-sheets compared to the control samples. This PBM-induced α-helix to β-sheet transition connects to reduced microtubule stability and the introduction of dynamism to allow for the remodeling and, consequently, refreshing of microtubule structures. This newly discovered mechanism could have implications for reducing the risks associated with brain aging, including neurodegenerative diseases like Alzheimer's disease, through the introduction of an intervention following this transition.

Experimental and Theoretical Approaches to Monitor the Behavior of Bovine Liver Catalase in Interaction with a Binuclear Bismuth Complex

Here, the antioxidant potency of a binuclear Bi(III) complex {[Bi2(μ-ox)(dipic)2(H2O)2 (taa)2].H2O, where ox2- = oxalato, dipic2- = pyridine 2,6-dicarboxylato, and taa = thiourea} was evaluated using the •DPPH assay. It was demonstrated that the Bi complex exhibited a high ability to inhibit DPPH free radicals. The binding mechanism of the complex with bovine liver catalase (BLC) was also investigated, revealing structural and activity changes in the enzyme in the presence of the complex. The catalase activity in the decomposition of hydrogen peroxide increased in the presence of the Bi complex, reaching 39.8% higher than its initial activity at a concentration of 7.77 × 10-6 M. The complex exhibited a relatively high affinity for BLC, with K b values of 3.98, 0.13, and 0.09 × 105 M-1 at 303, 310, and 317 K, respectively. The mechanisms involved in the interaction were hydrogen bonding and van der Waals interactions, as validated through molecular docking simulations. Synchronous fluorescence showed that tryptophan was more affected by enzyme-complex interactions than tyrosine. In addition, a cell viability test using the MTT method revealed that at its highest concentration, the Bi complex caused a decrease in the number of cells below 50% compared to the control, while cisplatin showed negative effects at all concentrations. These findings suggest that the Bi complex has the potential to be developed as a promising candidate for BLC-related therapeutic target therapy.

Keratin-PNIPAM Hybrid Microgels: Preparation, Morphology and Swelling Properties

Combinations of synthetic polymers, such as poly(N-isopropylacrylamide) (PNIPAM), with natural biomolecules, such as keratin, show potential in the field of biomedicine, since these hybrids merge the thermoresponsive properties of PNIPAM with the bioactive characteristics of keratin. This synergy aims to produce hybrids that can respond to environmental stimuli while maintaining biocompatibility and functionality, making them suitable for various medical and biotechnological uses. In this study, we exploit keratin derived from wool waste in the textile industry, extracted via sulfitolysis, to synthesize hybrids with PNIPAM microgel. Utilizing two distinct methods-polymerization of NIPAM with keratin (HYB-P) and mixing preformed PNIPAM microgels with keratin (HYB-M)-resulted in hybrids with 20% and 25% keratin content, respectively. Dynamic light scattering (DLS) and transmission electron microscopic (TEM) analyses indicated the formation of colloidal systems with particle sizes of around 110 nm for HYB-P and 518 nm for HYB-M. The presence of keratin in both systems, 20% and 25%, respectively, was confirmed by spectroscopic (FTIR and NMR) and elemental analyses. Distinct structural differences were observed between HYB-P and HYB-M, suggesting a graft copolymer configuration for the former hybrid and a complexation for the latter one. Furthermore, these hybrids demonstrated temperature responsiveness akin to PNIPAM microgels and pH responsiveness, underscoring their potential for diverse biomedical applications.

Isotope-Edited Variable Temperature Infrared Spectroscopy for Measuring Transition Temperatures of Single A-T Watson-Crick Base Pairs in DNA Duplexes

Experimental methods to determine transition temperatures for individual base pair melting events in DNA duplexes are lacking despite intense interest in these thermodynamic parameters. Here, we determine the dimensions of the thymine (T) C2═O stretching vibration when it is within the DNA duplex via isotopic substitutions at other atomic positions in the structure. First, we determined that this stretching state was localized enough to specific atoms in the molecule to make submolecular scale measurements of local structure and stability in high molecular weight complexes. Next, we develop a new isotope-edited variable temperature infrared method to measure melting transitions at various locations in a DNA structure. As an initial test of this "sub-molecular scale thermometer", we applied our T13C2 difference infrared signal to measure location-dependent melting temperatures (TmL) in a DNA duplex via variable temperature attenuated total reflectance Fourier transform infrared (VT-ATR-FTIR) spectroscopy. We report that the TmL of a single Watson-Crick A-T base pair near the end of an A-T rich sequence (poly T) is ∼34.9 ± 0.7°C. This is slightly lower than the TmL of a single base pair near the middle position of the poly T sequence (TmL ∼35.6±0.2°C). In addition, we also report that the TmL of a single Watson-Crick A-T base pair near the end of a 50% G-C sequence (12-mer) is ∼52.5 ± 0.3°C, which is slightly lower than the global melting Tm of the 12-mer sequence (TmL ∼54.0±0.9°C). Our results provide direct physical evidence for end fraying in DNA sequences with our novel spectroscopic methods.

Architectonic principles of polyproline II helix bundle protein domains

Glycine rich polyproline II helix assemblies are an emerging class of natural domains found in several proteins with different functions and diverse origins. The distinct properties of these domains relative to those composed of α-helices and β-sheets could make glycine-rich polyproline II helix assemblies a useful building block for protein design. Whereas the high population of polyproline II conformers in disordered state ensembles could facilitate glycine-rich polyproline II helix folding, the architectonic bases of these structures are not well known. Here, we compare and analyze their structures to uncover common features. These protein domains are found to be highly tolerant of distinct flanking sequences. This speaks to the robustness of this fold and strongly suggests that glycine rich polyproline II assemblies could be grafted with other protein domains to engineer new structures and functions. These domains are also well packed with few or no cavities. Moreover, a significant trend towards antiparallel helix configuration is observed in all these domains and could provide stabilizing interactions among macrodipoles. Finally, extensive networks of Cα-H···OC hydrogen bonds are detected in these domains. Despite their diverse evolutionary origins and activities, glycine-rich polyproline II helix assemblies share architectonic features which could help design novel proteins.

Propitious catalytic response of immobilized α-amylase from G. thermoleovorans in modified APTES-Fe3O4 NPs for industrial bio-processing

Challenges in enzyme and product recovery are currently intriguing in modern biotechnology. Coping enzyme stability, shelf life and efficiency, nanomaterials-based immobilization were epitomized of industrial practice. Herein, a α-amylase from Geobacillus thermoleovorans was purified and bound effectively on to a modified 3-Aminopropyltriethoxysilane (APTES)-Fe3O4 nanoparticle. It was revealed that the carrier-bound enzyme catalysis (pH 8 and 60 °C) was significant in contrast to the free enzyme (pH 7.5 and 55 °C). Furthermore, Zn2+ and Cu2+ were shown to cause inhibitory effects in both enzyme states. Unlike chloroform, toluene, benzene, and butanol, minimal effects were observed with ethanol, acetone, and hexane. The bound enzyme retained 27.4 % of its initial activity after being stored for 36 days. In addition, the reusability of the bound enzyme showed a gradual decline in activity after the first cycle; however, after 13 cycles, its residual activity at 53 % was observed. These data proved significant enough to use this enzyme for industrial starch and analogous substrate bio-processing.

Stem-Cell-Regenerative and Protective Effects of Squid (Symplectoteuthis oualaniensis) Skin Collagen Peptides against H2O2-Induced Fibroblast Injury

Recently, there has been a growing interest in collagen peptides derived from marine sources for their notable ability to protect skin cells against apoptosis induced by oxidants. Therefore, the current study aimed to investigate the fundamental properties of collagen peptides, including their physicochemical, thermal, structural, stem-cell-regenerative, and skin-cell-protective effects, in comparison to commercial collagen peptides. The acid-soluble (ASC) and pepsin-soluble (PSC) collagens exhibited three distinct bands on SDS-PAGE, namely α (α1 and α2), β, and γ chains, confirming a type I pattern. The thermal profiles obtained from TG and DSC analyses confirmed the denaturation of PSC and ASC at temperatures ranging from 51.94 to 56.4 °C and from 52.07 to 56.53 °C, respectively. The purified collagen peptides were analyzed using SDS-PAGE and MALDI-TOF mass spectrometry, revealing a mass range of 900-15,000 Da. Furthermore, the de novo peptide sequence analysis confirmed the presence of the Gly-X-Y repeating sequence in collagen peptides. Collagen peptide treatments significantly enhanced HFF-1 cell proliferation and migration compared to the control group. ELISA results confirmed the potential interactions between collagen peptides and HFF-1 cells through α2β1, α10β1, and α11β1 integrin receptors. Notably, collagen peptide treatment effectively restored the proliferation of HFF-1 cells damaged by H2O2. Consequently, the advantageous characteristics of squid skin collagen peptides highlight their promising role in regenerative medicine.

Accumulation and bio-oxidation of arsenite mediated by thermoacidophilic Cyanidiales: innate potential biomaterials toward arsenic remediation

Addressing geogenic and anthropogenic arsenic (As) pollution is critical for environmental health. This study explored arsenite [As(III)] removal using Cyanidiales, particularly Cyanidium caldarium (Cc) and Galdieria partita (Gp), under acidic to neutral pH, and determined As(III) detoxification mechanisms in relation to As speciation and protein secondary structure in Cyanidiales. Regarding As(III) sorption amounts, Cc outperformed Gp, reaching 83.2 mg g-1 of removal at pH 5.0. Wherein, 23.5 % of sorbed As on Cc presented as arsenate [As(V)] complexation with polysaccharides, alongside other predominant species including As(III)-cysteine (41.2 %) and As(III)-polysaccharides (35.3 %) complexes. This suggested that As(III) was directly transported into cells, rather than As(V). Coupled with the formation of As(III)-cysteine complexes within cells, these mechanisms may be key to efficiently accumulating As(III) in Cyanidiales during the 6-h incubation. These results highlight the potential of Cyanidiales for sustainable As(III) remediation and provide new insights into managing As(III) toxicity.

Unnatural Amino Acids for Biological Spectroscopy and Microscopy

Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.

Increased accuracy of vibrational circular dichroism calculations for isotopically labeled helical peptides

Vibrational circular dichroism (VCD) spectra have been computed with qualitatively correct sign patterns for α-helical peptides using various methods, ranging from empirical models to ab initio quantum mechanical computations. However, some details, such as deuteration effects and isotope substitution shifts and sign patterns for the resultant amide I' band shape, have remained a predictive challenge. Fully optimized computations for a 25-residue Ala-rich peptide, including implicit solvent corrections and explicit side chains that experimentally stabilize these model helical peptides in water, have been carried out using density functional theory (DFT). These fully minimized structures show minor changes in the (ϕ,ψ) torsions at the termini and yield an extra negative band to the low energy side of the characteristic amide I' couplet VCD, in agreement with experiments. Additionally, these calculations give the right sign and relative intensity patterns, as compared to experimental results, for several 13C=O substituted variants. The differences from previously reported computations that used ideal helical structures and vacuum conditions imply that inclusion of distorted termini and solvent effects can have an impact on the final detailed spectral patterns. Inclusion of side chains in these calculations had very little effect on the computed amide I' IR and VCD. Tests of constrained geometries, varying dielectric, and different functionals indicate that each can affect the band shapes, particularly for the 12C=O components, but these aspects do not fully explain the difference from previous spectral simulations. Inclusion of long-range amide coupling, as obtained from DFT computation of the full structure, or transfer of parameters from a somewhat longer peptide model, rather than shorter model, seems to be more important for the final detailed band shape under isotopic substitution. However, these corrections can also induce other changes, suggesting that previously reported, limited calculations may have been qualitatively useful due to a balance of errors. This may also explain the success of simple empirical IR models.

Unlocking the potential of SiO2 and CeO2 nanoparticles for arsenic mitigation in Vigna mungo L. Hepper (Blackgram)

In this study, the interaction effects of NaAsO2 (1 and 5 μM), SiO2 NPs (10 and 100 mg/L) and CeO2 NPs (10 and 100 mg/L) were assessed in Vigna mungo (Blackgram). The treatment of NaAsO2, SiO2, CeO2-NPs and combinations of NPs & As were applied to blackgram plants under hydroponic conditions. After its application, the morpho-physiological, antioxidant activity, and phytochemical study were evaluated. At 10 and 100 mg/L of SiO2 and CeO2-NPs, there was an increase in antioxidative enzymatic activity (p < 0.05) and reactive oxygen species (ROS). However, substantial ROS accumulation was observed at 1 and 5 μM NaAsO2 and 100 mg/L SiO2 NPs (p < 0.05). Additionally, at such concentrations, there is a substantial reduction in photosynthetic pigments, nitrogen fixation, chlorosis, and plant development when compared to controls (p < 0.05). The combination of SiO2 and CeO2 NPs (10 and 100 mg/L) with NaAsO2 decreased superoxide radical and hydrogen peroxide and improved SOD, CAT, APX, GR, and chlorophyll pigments (p < 0.05). Further FTIR results were evaluated for documenting elemental and phytochemical analysis.

Modulation of bacterial membranes and cellular macromolecules by dimethyl sulfoxide: A dose-dependent study providing novel insights

Using Escherichia coli as a model, this manuscript delves into the intricate interactions between dimethyl sulfoxide (DMSO) and membranes, cellular macromolecules, and the effects on various aspects of bacterial physiology. Given DMSO's wide-ranging use as a solvent in microbiology, we investigate the impacts of both non-growth inhibitory (1.0 % and 2.5 % v/v) and slightly growth-inhibitory (5.0 % v/v) concentrations of DMSO. The results demonstrate that DMSO causes alterations in bacterial membrane potential, influences the electrochemical characteristics of the cell surface, and exerts substantial effects on the composition and structure of cellular biomolecules. Genome-wide gene expression data from DMSO-treated E. coli was used to further investigate and bolster the results. The findings of this study provide valuable insights into the complex relationship between DMSO and biological systems, with potential implications in drug delivery and cellular manipulation. However, it is essential to exercise caution when utilizing DMSO to enhance the solubility and delivery of bioactive compounds, as even at low concentrations, DMSO exerts non-inert effects on cellular macromolecules and processes.

Synergistic impact of heat and salicylic acid pretreatment on gluten films: Characterization and functional properties

This study investigates how wheat gluten (WG) films in the presence of salicylic acid are influenced by thermal pretreatment. Unlike previous methods conducted at low moisture content, our procedure involves pretreating WG at different temperatures (65 °C, 75 °C, and 85 °C), in a solution with salicylic acid. This pretreatment aims to enhance protein unfolding, thus providing more opportunities for protein-protein interactions during the subsequent solvent casting into films. A significant increase in β-sheet structures was observed in FTIR spectra of samples pretreated at 75 °C and 85 °C, showing a prominent peak in the range of 1630-1640 cm-1. The pretreatment at 85 °C was found to be effective in improving the water resistivity of the films by up to 247 %. Moreover, it led to a significant enhancement of 151 % in tensile strength and a 45 % increase in the elastic modulus. The reduced solubility observed in films derived from pretreated WG suggests the development of an intricate protein network arising from protein-protein interactions during the pretreatment and film formation. Thermal pretreatment at 85 °C significantly enhances the structural and mechanical properties of WG films, including improved water resistivity, tensile strength, and intricate protein network formation.

The antimicrobial fibupeptide lugdunin forms water-filled channel structures in lipid membranes

Recently, a novel cyclo-heptapeptide composed of alternating D,L-amino acids and a unique thiazolidine heterocycle, called lugdunin, was discovered, which is produced by the nasal and skin commensal Staphylococcus lugdunensis. Lugdunin displays potent antimicrobial activity against a broad spectrum of Gram-positive bacteria, including challenging-to-treat methicillin-resistant Staphylococcus aureus (MRSA). Lugdunin specifically inhibits target bacteria by dissipating their membrane potential. However, the precise mode of action of this new class of fibupeptides remains largely elusive. Here, we disclose the mechanism by which lugdunin rapidly destabilizes the bacterial membrane potential using an in vitro approach. The peptide strongly partitions into lipid compositions resembling Gram-positive bacterial membranes but less in those harboring the eukaryotic membrane component cholesterol. Upon insertion, lugdunin forms hydrogen-bonded antiparallel β-sheets by the formation of peptide nanotubes, as demonstrated by ATR-FTIR spectroscopy and molecular dynamics simulations. These hydrophilic nanotubes filled with a water wire facilitate not only the translocation of protons but also of monovalent cations as demonstrated by voltage-clamp experiments on black lipid membranes. Collectively, our results provide evidence that the natural fibupeptide lugdunin acts as a peptidic channel that is spontaneously formed by an intricate stacking mechanism, leading to the dissipation of a bacterial cell's membrane potential.

High pressure Raman study of isobutyramide

Isobutyramide (IBA) has attracted considerable attention due to its expansive prospects for practical applications in the synthesis of drugs, dyes and other organic compounds. Herein we perform the high-pressure studies of IBA crystal by Raman spectral measurements at room temperature from ambient pressure to 30 GPa by using diamond anvil cells (DACs) to gain comprehensive insights into its structure and stability. Raman vibrational modes of IBA crystal at ambient pressure are resolved based on the experimental results and the first-principles theoretical calculations. High-pressure Raman scattering results show the Raman bands splitting, emergence/disappearance of the Raman bands and discontinuous wavenumber shifts at 1, 2 and 10 GPa, which indicate that IBA crystal undergoes three structural phase transitions at corresponding pressure. In addition, softening of the C = O and N-H stretching vibrational modes of IBA with increasing pressure can be interpreted by the reorganization of the hydrogen bond network of IBA molecules due to phase transition.

Colloidal surface-enhanced Raman spectroscopic study of grouper epidermal mucus using acidified sodium sulphate as the aggregating agent

Fish epidermal mucus is an important reservoir of antipathogenic compounds which serves as the first line of the immune defence. Despite its significant role in the physiology and health of fish, detailed profiling of fish epidermal mucus has yet to be explored. Therefore, this study investigates a label-free colloidal surface-enhanced Raman spectroscopic (SERS) method for profiling grouper mucus. Gold nanoparticles were first synthesised using the standard citrate reduction and characterised using ultraviolet-visible spectroscopy, transmission electron microscopy and dynamic light scattering. The influence of acidified sodium sulphate (Na2SO4) at pH 3 as the aggregating agent on the enhancement of the SERS spectrum of different analyte samples including rhodamine 6G (R6G) dye, lysozyme solution and hybrid grouper (Epinephelus fuscoguttatus × Epinephelus lanceolatus) mucus was observed. Based on the results, an optimal Na2SO4 concentration of 1 M was recorded to achieve the highest enhancement of the SERS signal for R6G and grouper mucus, while the optimal concentration for lysozyme was 0.1 M. The results indicated a higher degree of aggregation induced by lysozyme than R6G and grouper mucus. A few overlapping peaks of the SERS spectra of lysozyme and grouper mucus made it possible to confirm the presence of lysozyme as potential biomarkers.

Biochemical analysis of Hyalomma dromedarii salivary glands and gut tissues using SR-FTIR micro-spectroscopy

Ticks are obligatory voracious blood feeders infesting diverse vertebrate hosts, that have a crucial role in the transmission of diverse pathogens that threaten human and animal health. The continuous emergence of tick-borne diseases due to combined worldwide climatic changes, human activities, and acaricide-resistant tick strains, necessitates the development of novel ameliorative tick control strategies such as vaccines. The synchrotron-based Fourier transform infrared micro-spectroscopy (SR-FTIR) is a bioanalytical microprobe capable of exploring the molecular chemistry within microstructures at a cellular or subcellular level and is considered as a nondestructive analytical approach for biological specimens. In this study, SR-FTIR analysis was able to explore a qualitative and semi-quantitative biochemical composition of gut and salivary glands of Hyalomma dromedarii (H. dromedarii) tick detecting differences in the biochemical composition of both tissues. A notable observation regarding Amide I secondary structure protein profile was the higher ratio of aggregated strands in salivary gland and beta turns in gut tissues. Regarding the lipid profile, there was a higher intensity of lipid regions in gut tissue when compared to salivary glands. This detailed information on the biochemical compositions of tick tissues could assist in selecting vaccine and/or control candidates. Altogether, these findings confirmed SR-FTIR spectroscopy as a tool for detecting differences in the biochemical composition of H. dromedarii salivary glands and gut tissues. This approach could potentially be extended to the analysis of other ticks that are vectors of important diseases such as babesiosis and theileriosis.

Chasing weakly-bound biological water in aqueous environment near the peptide backbone by ultrafast 2D infrared spectroscopy

There has been a long-standing debate as to how many hydrogen bonds a peptide backbone amide can form in aqueous solution. Hydrogen-bonding structural dynamics of N-ethylpropionamide (a β-peptide model) in water was examined using infrared (IR) spectroscopy. Two amide-I sub bands arise mainly from amide C=O group that forms strong H-bonds with solvent water molecules (SHB state), and minorly from that involving one weak H-bond with water (WHB state). This picture is supported by molecular dynamics simulations and ab-initio calculations. Further, thermodynamics and kinetics of the SHB and WHB species were examined mainly by chemical-exchange two-dimensional IR spectroscopy, yielding an activation energy for the SHB-to-WHB exchange of 13.25 ± 0.52 kJ mol‒1, which occurs in half picosecond at room temperature. Our results provided experimental evidence of an unstable water molecule near peptide backbone, allowing us to gain more insights into the dynamics of the protein backbone hydration.

Predicting Cellular Rejection of Renal Allograft Based on the Serum Proteomic Fingerprint

Kidney transplantation is an essential medical procedure that significantly enhances the survival rates and quality of life for patients with end-stage kidney disease. However, despite advancements in immunosuppressive therapies, allograft rejection remains a leading cause of organ loss. Notably, predictions of cellular rejection processes primarily rely on biopsy analysis, which is not routinely performed due to its invasive nature. The present work evaluates if the serum proteomic fingerprint, as acquired by Fourier Transform Infrared (FTIR) spectroscopy, can predict cellular rejection processes. We analyzed 28 serum samples, corresponding to 17 without cellular rejection processes and 11 associated with cellular rejection processes, as based on biopsy analyses. The leave-one-out-cross validation procedure of a Naïve Bayes model enabled the prediction of cellular rejection processes with high sensitivity and specificity (AUC > 0.984). The serum proteomic profile was obtained in a high-throughput mode and based on a simple, rapid, and economical procedure, making it suitable for routine analyses and large-scale studies. Consequently, the current method presents a high potential to predict cellular rejection processes translatable to clinical scenarios, and that should continue to be explored.

Endogenous Production and Vibrational Analysis of Heavy-Isotope-Labeled Peptides from Cyanobacteria

Stable isotope labeling is an extremely useful tool for characterizing the structure, tracing the metabolism, and imaging the distribution of natural products in living organisms using mass-sensitive measurement techniques. In this study, a cyanobacterium was cultured in 15 N/13 C-enriched media to endogenously produce labeled, bioactive oligopeptides. The extent of heavy isotope incorporation in these peptides was determined with LC-MS, while the overall extent of heavy isotope incorporation in whole cells was studied with nanoSIMS and AFM-IR. Up to 98 % heavy isotope incorporation was observed in labeled cells. Three of the most abundant peptides, microcystin-LR (MCLR), cyanopeptolin-A (CYPA), and aerucyclamide-A (ACAA), were isolated and further studied with Raman and FTIR spectroscopies and DFT calculations. This revealed several IR and Raman active vibrations associated with functional groups not common in ribosomal peptides, like diene, ester, thiazole, thiazoline, and oxazoline groups, which could be suitable for future vibrational imaging studies. More broadly, this study outlines a simple and relatively inexpensive method for producing heavy-labeled natural products. Manipulating the bacterial culture conditions by the addition of specific types and amounts of heavy-labeled nutrients provides an efficient means of producing heavy-labeled natural products for mass-sensitive imaging studies.

Comparative Analysis of Macro/Microstructures and Constituents of Sorghum and Reed Straw

Node-containing straws exhibit superior mechanical properties compared to node-free straw plants, particularly in terms of shear resistance and compression resistance. We explore the relationship between the structure and mechanical properties of straw materials, providing deeper insights for the field of biomechanics. In this study, we focused on two node-containing straw plants, namely sorghum and reed. The main characteristics of sorghum and reed stalks were compared using macroscopic observation, stereomicroscopy, scanning electron microscopy, infrared spectroscopy, and EDS analysis. This study revealed numerous similarities and differences in the macro- and microstructures as well as the elemental composition of sorghum and reed stalks. The functional groups in sorghum and reed stalks were largely similar, with the primary elements being C and O. Distinguishing features included a higher tapering and a slightly larger reduction in wall thickness in sorghum stalks compared to reed stalks. The cross-section of sorghum stalks was filled with pith structures, while reed stalks exhibited a hollow structure. The vascular bundles in sorghum typically showed a paired arrangement, whereas those in reeds were arranged in odd numbers. Furthermore, sorghum straws contained more Cl and no Br, while the parenchyma of reed straws contained higher Br. The C and O proportions of sorghum straws and reed straws are 50-53% (50-51%) and 45-46% (48-49%), respectively. These variations in elemental composition are believed to be correlated with the mechanical properties of the materials. By conducting a detailed study of the micro/macrostructures and material composition of sorghum and reed straw, this paper provides valuable insights for the field of biomechanics.

Determining the nanostructure and main axis of gly-his-gly fibrils using the amide I' bands in FTIR, VCD, and Raman spectra

The zwitterionic tripeptide glycyl-histidine-glycine (GHG) has been shown to self-assemble into visible crystalline fibrils that form a gel-supporting network with a very high storage modulus. Here we elaborate on the theory and experimental setup behind our novel approach employed to determining the main fibril axis for these gel-forming fibrils by simulating the amide I band profile for infrared absorption (IR), vibrational circular dichroism (VCD), and visible Raman scattering. We also highlight that combining these three vibrational spectroscopies can help in validating structures that are solved using powder x-ray diffraction analysis (PXRD). The PXRD analysis yielded a GHG fibril unit cell with P21 symmetry containing two peptide monomers and two water molecules. The monomers adopt a conformation reminiscent of the distorted polyproline II conformation obtained for tri-lysine in aqueous solution. Stabilization occurs primarily through peptide-peptide intermolecular hydrogen bond interactions, while the role of water in peptide hydration is minimal. The comparison of simulated and experimental amide I' band profiles suggests that the xz plane of the crystal unit cell is being predominantly probed in the experimental IR and VCD spectra, with the x axis of the unit cell pointing in the direction of the main fibril axis. The monomer peptide in the unit cell interacts with six adjacent peptides forming hydrophobic channels by edge-to-face and parallel-displaced ππstacking in the y direction. These cores are further stabilized by a plethora of intermolecular interactions in the x and z directions. Our result suggests that the hydrophobic xz-surfaces would be a good target for the adsorption of hydrophobic drugs.

Interaction of food colorant indigo carmine with human and bovine serum albumins: A multispectroscopic, calorimetric, and theoretical investigation

In this work we have studied the interaction of the food dye Indigo-Carmine (IndC) with the most studied model transport proteins i.e. human and bovine serum albumin (HSA & BSA). A multispectroscopic approach was used to analyze the details of the binding process. The intrinsic fluorescence of both the albumins was significantly quenched by IndC and the quenching was both static and dynamic in nature with the former being dominant. The HSA-lndC and BSA-IndC distance after complexation was determined by Förster resonance energy transfer (FRET) method which suggested efficient energy transfer from the albumins to IndC. Thermodynamics of serum protein-IndC complexation was estimated by isothermal titration calorimetry (ITC) which revealed that the binding was enthalpy driven. Circular dichroism (CD) and FTIR spectroscopy revealed that the binding of IndC induced secondary structural changes in both the serum proteins. Synchronous and 3D fluorescence spectroscopy revealed that the binding interaction caused microenvironmental changes of protein fluorophores. Molecular docking analysis suggested that hydrogen bonding and hydrophobic interactions are the major forces involved in the complexation process.

Uncovering supramolecular chirality codes for the design of tunable biomaterials

In neurodegenerative diseases, polymorphism and supramolecular assembly of β-sheet amyloids are implicated in many different etiologies and may adopt either a left- or right-handed supramolecular chirality. Yet, the underlying principles of how sequence regulates supramolecular chirality remains unknown. Here, we characterize the sequence specificity of the central core of amyloid-β 42 and design derivatives which enable chirality inversion at biologically relevant temperatures. We further find that C-terminal modifications can tune the energy barrier of a left-to-right chiral inversion. Leveraging this design principle, we demonstrate how temperature-triggered chiral inversion of peptides hosting therapeutic payloads modulates the dosed release of an anticancer drug. These results suggest a generalizable approach for fine-tuning supramolecular chirality that can be applied in developing treatments to regulate amyloid morphology in neurodegeneration as well as in other disease states.

Production and characterization of human hair keratin bioplastic films with novel plasticizers

Since their invention, conventional plastics have contributed in the betterment of the society in numerous ways, nevertheless their deleterious impacts on the natural ecosystems and living creatures is irrefutable. The management of plastic waste generated is a concern worldwide and therefore quest for the plastic alternates or bioplastics is imminent. Here, we explore the suitability of keratin from human hair waste as the candidate for the production of bioplastic films. Keratin extracted from hair was used to form the films or 'kertics' by solution casting and curing. Ethanediol, di-ethylene glycol and tri-ethylene glycol were used as novel plasticizers along with glycerol in the keratin film formation. The film prepared were of the thickness 190-220 µm with the area of about 4.54 ± 0.2 cm2. Water uptake by G100, ED100, DEG100 and TEG100 films was recorded to be 4.8, 6.2, 4.9 and 6.3% respectively. FESEM analysis revealed that the films with 100 µl of 1% glycerol (G100) had continuous surface morphology except few pits of 0.1 µm, also DEG100 and TEG100 films have the most uniform surface morphology with no evident pits, holes or bulges. X-ray diffractogram showed characteristic peak of keratin at 19.5° and the d-spacing value observed was 0.45 nm. The FTIR studies suggested that the films retained keratin in non degraded form, and possessed the characteristic Amide peaks. The films were also found to be biodegradable in studies involving keratinophilic fungal strain of A. oryzae. These films could found potential applications in packaging industry, disposable items manufacturing and biomaterial generation.

Raman spectroscopy and its plasmon-enhanced counterparts: A toolbox to probe protein dynamics and aggregation

Protein unfolding and aggregation are often correlated with numerous diseases such as Alzheimer's, Parkinson's, Huntington's, and other debilitating neurological disorders. Such adverse events consist of a plethora of competing mechanisms, particularly interactions that control the stability and cooperativity of the process. However, it remains challenging to probe the molecular mechanism of protein dynamics such as aggregation, and monitor them in real-time under physiological conditions. Recently, Raman spectroscopy and its plasmon-enhanced counterparts, such as surface-enhanced Raman spectroscopy (SERS) and tip-enhanced Raman spectroscopy (TERS), have emerged as sensitive analytical tools that have the potential to perform molecular studies of functional groups and are showing significant promise in probing events related to protein aggregation. We summarize the fundamental working principles of Raman, SERS, and TERS as nondestructive, easy-to-perform, and fast tools for probing protein dynamics and aggregation. Finally, we highlight the utility of these techniques for the analysis of vibrational spectra of aggregation of proteins from various sources such as tissues, pathogens, food, biopharmaceuticals, and lastly, biological fouling to retrieve precise chemical information, which can be potentially translated to practical applications and point-of-care (PoC) devices. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Diagnostic Tools > Diagnostic Nanodevices Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.

Spectroscopic Analysis of the Effect of Ibuprofen Degradation Products on the Interaction between Ibuprofen and Human Serum Albumin

BACKGROUND

Non-Steroidal Anti-Inflammatory Drugs (NSAIDs) are one of the most commonly used groups of medicinal compounds in the world. The wide access to NSAIDs and the various ways of storing them due to their easy accessibility often entail the problem with the stability and durability resulting from the exposure of drugs to external factors. The aim of the research was to evaluate in vitro the mechanism of competition between ibuprofen (IBU) and its degradation products, i.e., 4'-isobutylacetophenone (IBAP) and (2RS)-2-(4- formylphenyl)propionic acid (FPPA) during transport in a complex with fatted (HSA) and defatted (dHSA) human serum albumin.

METHODS

The research was carried out using spectroscopic techniques, such as spectrophotometry, infrared spectroscopy and nuclear magnetic resonance spectroscopy.

RESULTS

The comprehensive application of spectroscopic techniques allowed, among others, for the determination of the binding constant, the number of classes of binding sites and the cooperativeness constant of the analyzed systems IBU-(d)HSA, IBU-(d)HSA-FPPA, IBU-(d)HSA-IBAP; the determination of the effect of ibuprofen and its degradation products on the secondary structure of albumin; identification and assessment of interactions between ligand and albumin; assessment of the impact of the presence of fatty acids in the structure of albumin and the measurement temperature on the binding of IBU, IBAP and FPPA to (d)HSA.

CONCLUSION

The conducted research allowed us to conclude that the presence of ibuprofen degradation products and the increase in their concentration significantly affect the formation of the IBU-albumin complex and thus, the value of the association constant of the drug, changing the concentration of its free fraction in the blood plasma. It was also found that the presence of an ibuprofen degradation product in a complex with albumin affects its secondary structure.

Structure specific neuro-toxicity of α-synuclein oligomer

Parkinson's disease (PD) is linked to α-synuclein (aS) aggregation and deposition of amyloid in the substantia nigra region of the brain tissues. In the current investigation we produced two distinct classes of aS oligomer of differed protein conformation, stability and compared their toxic nature to cultured neuronal cells. Lyophilized oligomer (LO) was produced in storage of aS at-20 °C for 7 days and it was enriched with loosely hold molten globule like structure with residues having preferences for α-helical conformational space. The size of the oligomer was 4-5.5 nm under AFM. This kind of oligomer exhibited potential toxicity towards neuronal cell lines and did not transform into compact β-sheet rich amyloid fiber even after incubation at 37 °C for several days. Formation of another type of oligomer was often observed in the lag phase of aS fibrillation that often occurred at an elevated temperature (37 °C). This kind of heat induced oligomer (IO) was more hydrophobic and relatively less toxic to neuronal cells compared to lyophilized oligomer (LO). Importantly, initiation of hydrophobic zipping of aS caused the transformation of IO into thermodynamically stable β-sheet rich amyloid fibril. On the other hand, the presence of molten globule like conformation in LO, rendered greater toxicity to cultured neuronal cells.

Wheat gluten amyloid fibrils: Conditions, mechanism, characterization, application, and future perspectives

Amyloid fibrils have excellent structural characteristics, such as a high aspect ratio, excellent stiffness, and a wide availability of functional groups on the surface. More studies are now focusing on the formation of amyloid fibrils using food proteins. Protein fibrillation is now becoming recognized as a promising strategy for enhancing the function of food proteins and expanding their range of applications. Wheat gluten is rich in glutamine (Q), hydrophobic amino acids, and the α-helix structure with high β-sheet tendency. These characteristics make it very easy for wheat gluten to form amyloid fibrils. The conditions, formation mechanism, characterization methods, and application of amyloid fibrils formed by wheat gluten are summarized in this review. Further exploration of amyloid fibrils formed by wheat gluten will reveal how they can play a significant role in food, biology, and other fields, especially in medicine.

Development and evaluation of tilapia skin-derived gelatin, collagen, and acellular dermal matrix for potential use as hemostatic sponges

Hemostasis plays a critical role in the early stage of wound healing, especially in acute wounds which can significantly improve the survival of patients. Based on the excellent biocompatibility of natural biomaterials, in this study, we prepared a series of novel hemostatic sponges by using tilapia skin, a marine biological resource, and extracting tilapia skin-derived gelatin, collagen, and acellular dermal matrix through five different methods. Using in vitro sheep blood and in vivo rat liver hemorrhage models, we found that tilapia skin sponges had excellent coagulation and hemostatic abilities. Among them, the collagen sponge exhibited optimal hemostasis performance because it could accelerate clotting by binding to the specific sites of blood cells and platelets. Furthermore, the sponges' porous structure enhanced the capability to absorb blood, thus effectively promoting hemostasis. In summary, we reported an efficient and convenient method to prepare marine biological resources into sponges, which provided a novel class of alternatives for hemostasis in acute wounds with broad application prospects.

Umbrella-like Helical Structure of α-Synuclein at the Air-Water Interface Observed with Experimental and Theoretical Sum Frequency Generation Spectroscopy

The misfolding of α-synuclein (αS) into amyloid aggregates is catalyzed by hydrophobic surfaces and associated with severe brain disorders, such as Parkinson's disease. Despite the important role of interfaces, the three-dimensional structure of αS at the interfaces is still not clear. We report interface-specific sum frequency generation (SFG) experiments of monomeric αS binding to the air-water interface, a model system for the important hydrophobic surfaces. We combine the SFG spectra with calculations of theoretical spectra based on molecular dynamics simulations to show that αS, which is an intrinsically disordered protein in solution, folds into a defined, mostly helical secondary structure at the air-water interface. The binding pose resembles an umbrella shape, where the C-terminus protrudes into the water phase, while the N-terminus and the NAC region span the canopy at the interface. In this binding pose, αS is prone to aggregate, which could explain the catalytic effect of hydrophobic interfaces and air bubbles on αS fibrillation.

Liquid-Liquid Phase Separation of the Intrinsically Disordered Domain of the Fused in Sarcoma Protein Results in Substantial Slowing of Hydration Dynamics

Formation of liquid condensates plays a critical role in biology via localization of different components or via altered hydrodynamic transport, yet the hydrogen-bonding environment within condensates, pivotal for solvation, has remained elusive. We explore the hydrogen-bond dynamics within condensates formed by the low-complexity domain of the fused in sarcoma protein. Probing the hydrogen-bond dynamics sensed by condensate proteins using two-dimensional infrared spectroscopy of the protein amide I vibrations, we find that frequency-frequency correlations of the amide I vibration decay on a picosecond time scale. Interestingly, these dynamics are markedly slower for proteins in the condensate than in a homogeneous protein solution, indicative of different hydration dynamics. All-atom molecular dynamics simulations confirm that lifetimes of hydrogen-bonds between water and the protein are longer in the condensates than in the protein in solution. Altered hydrogen-bonding dynamics may contribute to unique solvation and reaction dynamics in such condensates.

Thin-Film Waveguide Laser Spectroscopy: A Novel Platform for Bacterial Analysis

Bacterial sensing based on quantum cascade laser spectroscopy coupled with diamond or gallium arsenide thin-film waveguides is a novel analytical tool for gaining high-resolution infrared spectroscopic information of planktonic and sessile bacteria, as shown in the present study for Escherichia coli. During observation periods of up to 24 h, diamond and gallium arsenide thin-film waveguide laser spectroscopy was compared to information obtained via conventional Fourier transform infrared spectroscopy. The proliferation behavior of E. coli at those surfaces was complementarily investigated using atomic force microscopy and scanning electron microscopy.

Structural Dependence of Extended Amide III Vibrations in Two-Dimensional Infrared Spectra

Two-dimensional infrared (2D-IR) spectroscopy is a powerful experimental method for probing the structure and dynamics of proteins in aqueous solution. So far, most experimental studies have focused on the amide I vibrations, for which empirical vibrational exciton models provide a means of interpreting such experiments. However, such models are largely lacking for other regions of the vibrational spectrum. To close this gap, we employ an efficient quantum-chemical methodology for the calculation of 2D-IR spectra, which is based on anharmonic theoretical vibrational spectroscopy with localized modes. We apply this approach to explore the potential of 2D-IR spectroscopy in the extended amide III region. Using calculations for a dipeptide model as well as alanine polypeptides, we show that distinct 2D-IR cross-peaks in the extended amide III region can potentially be used to distinguish α-helix and β-strand structures. We propose that the extended amide III region could be a promising target for future 2D-IR experiments.

Ambidexterity and Left-Handedness Induced by Geminally Disubstituted γ Amino Acid Residues in Chiral 310 Helices

Chirality is an omnipresent feature in nature's architecture starting from simple molecules like amino acids to complex higher-order structures viz. proteins, DNA, and RNA. The L configuration of proteinogenic amino acids gives rise to right-handed helices. Ambidexterity is as rare in organisms as in molecules. There are only a few reports of ambidexterity in single-peptide molecules composed of either mixed L and D or achiral residues. Here, we report, for the first time, the ambidextrous and left-handed helical conformations in the chiral nonapeptides P1-P3 (Boc-LUVUγx,xULUV-OMe where U = Aib, x,x = 2,2/3,3/4,4), containing chiral L α amino acid residues, in addition to the usually observed right-handed helical conformation. The centrally located achiral γ residue, capable of adopting both left and right-handed helical conformations, induces its handedness on the neighboring chiral and achiral residues, leading to the observation of both left and right-handed helices in P2 and P3. The presence of a single water molecule proximal to the γ residue induces the reversal of helix handedness by forming distinct and stable water-mediated hydrogen bonds. This gives rise to ambidextrous helices as major conformers in P1 and P2. The absence of the observation of ambidexterity in P3 might be due to the inability of γ4,4 in the recruitment of a water molecule. Experiments (NMR, X-ray, and CD) and density functional theory (DFT) calculations suggest that the position of geminal disubstitution is crucial for determining the population of the amenable helical conformations (ambidextrous, left and right-handed) in these chiral peptides.

Combined In Silico and In Vitro Study to Reveal the Structural Insights and Nucleotide-Binding Ability of the Transcriptional Regulator PehR from the Phytopathogen Ralstonia solanacearum

The transcriptional regulator PehR regulates the synthesis of the extracellular plant cell wall-degrading enzyme polygalacturonase, which is essential in the bacterial wilt of plants caused by one of the most devastating plant phytopathogens, Ralstonia solanacearum. The bacterium has a wide global distribution infecting many different plant species, resulting in massive agricultural and economic losses. Because the PehR molecular structure has not yet been determined and the structural consequences of PehR on ligand binding have not been thoroughly investigated, we have used an in silico approach combined with in vitro experiments for the first time to characterize the PehR regulator from a local isolate (Tezpur, Assam, India) of the phytopathogenic bacterium R. solanacearum F1C1. In this study, an in silico approach was employed to model the 3D structure of the PehR regulator, followed by the binding analysis of different ligands against this regulatory protein. Molecular docking studies suggest that ATP has the highest binding affinity for the PehR regulator. By using molecular dynamics (MD) simulation analysis, involving root-mean-square deviation, root-mean-square fluctuations, hydrogen bonding, radius of gyration, solvent-accessible surface area, and principal component analysis, it was possible to confirm the sudden conformational changes of the PehR regulator caused by the presence of ATP. We used an in vitro approach to further validate the formation of the PehR-ATP complex. In this approach, recombinant DNA technology was used to clone, express, and purify the gene encoding the PehR regulator from R. solanacearum F1C1. Purified PehR was used in ATP-binding experiments using fluorescence spectroscopy and Fourier transform infrared spectroscopy, the outcomes of which showed a potent binding to ATP. The putative PehR-ATP-binding analysis revealed the importance of the amino acids Lys190, Glu191, Arg192, Arg375, and Asp378 for the ATP-binding process, but further study is required to confirm this. It will be simpler to comprehend the catalytic mechanisms of a crucial PehR regulator process in R. solanacearum with the aid of the ATP-binding process hints provided by these structural biology applications.

Scanning Tunneling Microscopy Study of Lipoic Acid, Mannose, and cRGD@AuNPs Conjugates

The functionalization of AuNPs with different biological elements was achieved to investigate their possibility in biomedical applications such as drug delivery, vaccine development, sensing, and imaging. Biofunctionalized AuNPs are pursued for applications such as drug delivery, vaccine development, sensing, and imaging. In this study, AuNPs with diameters of 20 nm were functionalized with lipoic acid, mannose, or the cRGD peptide. By using UV-vis spectroscopy, Fourier transform infrared spectroscopy, dynamic light scattering, transmission electron microscopy, and scanning tunneling microscopy techniques, we showed that AuNPs can be functionalized by these biomolecules in a reliable way to obtain conjugates to explore potential biomedical applications. In particular, we demonstrate that the STM technique can be employed to analyze biofunctionalized AuNPs, and the obtained information can be valuable in the design of biomedical applications.

Conformational Manifold Sampled by Two Short Linear Motif Segments Probed by Circular Dichroism, Vibrational, and Nuclear Magnetic Resonance Spectroscopy

Disordered protein segments called short linear motifs (SLiM) serve as recognition sites for a variety of biological processes and act as targeting signals, modification, and ligand binding sites. While SLiMs do not adopt one of the known regular secondary structures, the conformational distribution might still reflect the structural propensities of their amino acid residues and possible interactions between them. In the past, conformational analyses of short peptides provided compelling evidence for the notion that individual residues are less conformationally flexible than locally expected for a random coil. Here, we combined various spectroscopies (NMR, IR, vibrational, and UV circular dichroism) to determine the Ramachandran plots of two SLiM motifs, i.e., GRRDSG and GRRTSG. They are two representatives of RxxS motifs that are capable of being phosphorylated by protein kinase A, an enzyme that plays a fundamental role in a variety of biological processes. Our results reveal that the nearest and non-nearest interactions between residues cause redistributions between polyproline II and β-strand basins while concomitantly stabilizing extended relative to turn-forming and helical structures. They also cause shifts in basin positions. With increasing temperature, β-strand populations become more populated at the expense of polyproline II. While molecular dynamics simulations with Amber ff14SB and CHARMM 36m force fields indicate residue-residue interactions, they do not account for the observed structural changes.

Crowding alters F-actin secondary structure and hydration

Actin, an important component of eukaryotic cell cytoskeleton, regulates cell shape and transport. The morphology and biochemical properties of actin filaments are determined by their structure and protein-protein contacts. Crowded environments can organize filaments into bundles, but less is known about how they affect F-actin structure. This study used 2D IR spectroscopy and spectral calculations to examine how crowding and bundling impact the secondary structure and local environments in filaments and weakly or strongly bundled networks. The results reveal that bundling induces changes in actin's secondary structure, leading to a decrease in β-sheet and an increase in loop conformations. Strongly bundled networks exhibit a decrease in backbone solvent exposure, with less perturbed α-helices and nearly "locked" β-sheets. Similarly, the loops become less hydrated but maintain a dynamic environment. These findings highlight the role of loop structure in actin network morphology and stability under morphology control by PEG.

Purification and fractionation of phycobiliproteins from Arthrospira platensis and Corallina officinalis with evaluating their biological activities

Phycobiliproteins (PBPs) are a class of water-soluble pigments with a variety of biological functions that are present in red macroalgae and cyanobacterial species. The crude forms of phycocyanin (C-PC) from the blue green alga Arthrospira platensis and allophycocyanin (APC) from the red macroalga Corallina officinalis were extracted and purified by ammonium sulphate precipitation, anion exchange chromatography, and size exclusion chromatography methods, respectively. The obtained C-PC and APC from A. platensis and C. officinalis were 0.31 mg/mL and 0.08 mg/mL, respectively, with molecular masses of "17.0 KDa and 19.0 KDa" and "15.0 KDa and 17.0 KDa" corresponding to α and β subunits, respectively. FT-IR was used to characterize the purified APC and C-PC in order to look into their structures. Highly purified extracts (A620/A280 > 4.0) were obtained from subtractions' PC3 and PC4 that were tested for their biological activities. APC and C-PC crude extracts plus their fractions exhibited potent anti-oxidant in different ratios by using three techniques. PC1 showed high anti-inflammatory (75.99 and 74.55%) and anti-arthritic (78.89 and 76.92%) activities for C. officinalis and A. platensis, respectively compared with standard drugs (72.02 and 71.5%). The methanolic and water extracts of both species showed greater antibacterial efficacy against Gram +ve than Gram -ve marine bacteria. Our study shed light on the potential medical uses of C-PC and APC extracted from the tested species as natural substances in a variety of foods and drugs. Further investigations are required to explore the diverse chemical natures of distinct PBPs from different cyanobacteria and red algae because their amino acid sequences vary among different algal species.

Kinetic control in amyloid polymorphism: Different agitation and solution conditions promote distinct amyloid polymorphs of alpha-synuclein

Aggregation of neuronal protein α-synuclein is implicated in synucleinopathies, including Parkinson's disease. Despite abundant in vitro studies, the mechanism of α-synuclein assembly process remains ambiguous. In this work, α-synuclein aggregation was induced by its constant mixing in two separate modes, either by agitation in a 96-well microplate reader (MP) or in microcentrifuge tubes using a shaker incubator (SI). Aggregation in both modes occurred through a sigmoidal growth pattern with a well-defined lag, growth, and saturation phase. The end-stage MP- and SI-derived aggregates displayed distinct differences in morphological, biochemical, and spectral signatures as discerned through AFM, proteinase-K digestion, FTIR, Raman, and CD spectroscopy. The MP-derived aggregates showed irregular morphology with a significant random coil conformation, contrary to SI-derived aggregates, which showed typical β-sheet fibrillar structures. The end-stage MP aggregates convert to β-rich SI-like aggregates upon 1) seeding with SI-derived aggregates and 2) agitating in SI. We conclude that end-stage MP aggregates were in a kinetically trapped conformation, whose kinetic barrier was bypassed upon either seeding by SI-derived fibrils or shaking in SI. We further show that MP-derived aggregates that form in the presence of sorbitol, an osmolyte, displayed a β-rich signature, indicating that the preferential exclusion effect of osmolytes helped overcome the kinetic barrier. Our findings help in unravelling the kinetic origin of different α-synuclein aggregated polymorphs (strains) that encode diverse variants of synucleinopathies. We demonstrate that kinetic control shapes the polymorphic landscape of α-synuclein aggregates, both through de novo generation of polymorphs, and by their interconversion.

Underwater Bonding with a Biobased Adhesive from Tannic Acid and Zein Protein

Herein are presented several adhesive formulations made from zein protein and tannic acid that can bind to a wide range of surfaces underwater. Higher performance comes from more tannic acid than zein, whereas dry bonding required the opposite case of more zein than tannic acid. Each adhesive works best in the environment that it was designed and optimized for. We show underwater adhesion experiments done on different substrates and in different waters (sea water, saline solution, tap water, deionized water). Surprisingly, the water type does not influence the performance to a great deal but the substrate type does. An additional unexpected result was bond strength increasing over time when exposed to water, contradicting general experiments of working with glues. Initial adhesion underwater was stronger compared to benchtop adhesion, suggesting that water helps to make the glue stick. Temperature effects were determined, indicating maximum bonding at about 30 °C and then another increase at higher temperatures. Once the adhesive was placed underwater, a protective skin formed on the surface, keeping water from entering the rest of the material immediately. The shape of the adhesive could be manipulated easily and, once in place, the skin could be broken to induce faster bond formation. Data indicated that underwater adhesion was predominantly induced by tannic acid, cross-linking within the bulk for adhesion and to the substrate surfaces. The zein protein provided a less polar matrix that helped to keep the tannic acid molecules in place. These studies provide new plant-based adhesives for working underwater and for creating a more sustainable environment.

Unpolarized laser method for infrared spectrum calculation of amide I CO bonds in proteins using molecular dynamics simulation

The investigation of the strong infrared (IR)-active amide I modes of peptides and proteins has received considerable attention because a wealth of detailed information on hydrogen bonding, dipole-dipole interactions, and the conformations of the peptide backbone can be derived from the amide I bands. The interpretation of experimental spectra typically requires substantial theoretical support, such as direct ab-initio molecular dynamics simulation or mixed quantum-classical description. However, considering the difficulties associated with these theoretical methods and their applications are limited in small peptides, it is highly desirable to develop a simple yet efficient approach for simulating the amide I modes of any large proteins in solution. In this work, we proposed a comprehensive computational method that extends the well-established molecular dynamics (MD) simulation method to include an unpolarized IR laser for exciting the CO bonds of proteins. We showed the amide I frequency corresponding to the frequency of the laser pulse which resonated with the CO bond vibration. At this frequency, the protein energy and the CO bond length fluctuation were maximized. Overall, the amide I bands of various single proteins and amyloids agreed well with experimental data. The method has been implemented into the AMBER simulation package, making it widely available to the scientific community. Additionally, the application of the method to simulate the transient amide I bands of amyloid fibrils during the IR laser-induced disassembly process was discussed in details.

Quantum Cascade Laser Based Infrared Spectroscopy: A New Paradigm for Protein Secondary Structure Measurement

Mid-infrared spectroscopy is one of the major analytical techniques employed for measurements of protein structure in solution. Traditional Fourier Transform-Infrared (FT-IR) measurement is limited by its blackbody light source that is inherently spatially incoherent and has low optical power output. This limitation is pronounced when working with proteins in aqueous solutions. Strong absorbance of water in protein amide I region 1600-1700 cm-1 restricts light path length to <10 μm and imposes significant experimental challenges in sample and flow cell handling. Emerging laser spectroscopic techniques use high-power coherent laser as light source that overcomes the limitation in FT-IR measurement. In this study, we employed an innovative infrared spectrometer that uses quantum cascade laser (QCL) as light source. Continuous infrared radiation from this laser source can be swiftly swept within the amide I region (1600-1700 cm-1) and amide II region (1500-1600 cm-1), which makes this technique ideal for protein secondary structure study. Protein solutions as low as 0.5 mg/mL were measured rapidly without any sample preparation. Infrared spectra of model proteins were thus collected, and a chemometric model based on partial least squares regression was developed to quantify α-helix and β-strand motifs in protein secondary structure. The model was applied to measurement of the native secondary structure of commercial therapeutic proteins and bovine serum albumin (BSA) and in thermal degradation studies.

Recent development of surface-enhanced Raman scattering for biosensing

Surface-Enhanced Raman Scattering (SERS) technology, as a powerful tool to identify molecular species by collecting molecular spectral signals at the single-molecule level, has achieved substantial progresses in the fields of environmental science, medical diagnosis, food safety, and biological analysis. As deepening research is delved into SERS sensing, more and more high-performance or multifunctional SERS substrate materials emerge, which are expected to push Raman sensing into more application fields. Especially in the field of biological analysis, intrinsic and extrinsic SERS sensing schemes have been widely used and explored due to their fast, sensitive and reliable advantages. Herein, recent developments of SERS substrates and their applications in biomolecular detection (SARS-CoV-2 virus, tumor etc.), biological imaging and pesticide detection are summarized. The SERS concepts (including its basic theory and sensing mechanism) and the important strategies (extending from nanomaterials with tunable shapes and nanostructures to surface bio-functionalization by modifying affinity groups or specific biomolecules) for improving SERS biosensing performance are comprehensively discussed. For data analysis and identification, the applications of machine learning methods and software acquisition sources in SERS biosensing and diagnosing are discussed in detail. In conclusion, the challenges and perspectives of SERS biosensing in the future are presented.

The relevance of short peptides for an understanding of unfolded and intrinsically disordered proteins

Over the last thirty years the unfolded state of proteins has attracted considerable interest owing to the discovery of intrinsically disordered proteins which perform a plethora of functions despite resembling unfolded proteins to a significant extent. Research on both, unfolded and disordered proteins has revealed that their conformational properties can deviate locally from random coil behavior. In this context results from work on short oligopeptides suggest that individual amino acid residues sample the sterically allowed fraction of the Ramachandran plot to a different extent. Alanine has been found to exhibit a peculiarity in that it has a very high propensity for adopting polyproline II like conformations. This Perspectives article reviews work on short peptides aimed at exploring the Ramachandran distributions of amino acid residues in different contexts with experimental and computational means. Based on the thus provided overview the article discussed to what extent short peptides can serve as tools for exploring unfolded and disordered proteins and as benchmarks for the development of a molecular dynamics force field.